Editing Convergent evolution (section)

==At molecular level==
[[File:Triad convergence ser cys.svg|thumb|upright=1.5|Evolutionary convergence of [[serine protease|serine]] and [[cysteine protease]] towards the same catalytic triads organisation of acid-base-nucleophile in different [[protein superfamily|protease superfamilies]]. Shown are the triads of [[subtilisin]], [[prolyl oligopeptidase]], [[TEV protease]], and [[papain]].]]

===Proteins===

====Tertiary structures====

Many proteins share analogous [[Protein structure|structural elements]] that arose independently across different genomes. There are several examples of convergent protein motifs sharing similar arrangements of structural elements.<ref>{{cite journal |last=Cheng |first=H. |last2=Kim |first2=B-H. |last3=Grishin |first3=N. V. |title=MALISAM: a database of structurally analogous motifs in proteins |journal=Nucleic Acids Research |date=September 2008 |volume=36 |pages=211–217 |pmid=17855399 |doi=10.1093/nar/gkm698 |pmc=2238938}}</ref> Whole protein structures too have arisen through convergent evolution.<ref>{{cite journal |last=Wright |first=E. S. |title=Tandem repeats provide evidence for convergent evolution to similar protein structures |journal=Genome Biology and Evolution |date=January 2025 |pmid=39852593 |doi=10.1093/gbe/evaf013|doi-access=free |pmc=11812678 }}</ref>

====Protease active sites====

The [[enzymology]] of [[proteases]] provides some of the clearest examples of convergent evolution. These examples reflect the intrinsic chemical constraints on enzymes, leading evolution to converge on equivalent solutions independently and repeatedly.<ref name="Buller&Townsend_2013"/><ref>{{cite journal |last=Dodson |first=G. |author2=Wlodawer, A. |title=Catalytic triads and their relatives |journal=Trends in Biochemical Sciences |date=September 1998 |volume=23 |issue=9 |pages=347–52 |pmid=9787641 |doi=10.1016/S0968-0004(98)01254-7}}</ref>

Serine and cysteine proteases use different amino acid functional groups (alcohol or thiol) as a [[nucleophile]]. To activate that nucleophile, they orient an acidic and a basic residue in a [[catalytic triad]]. The chemical and physical constraints on [[enzyme catalysis]] have caused identical triad arrangements to evolve independently more than 20 times in different [[enzyme superfamilies]].<ref name="Buller&Townsend_2013"/>

[[Threonine protease]]s use the amino acid threonine as their catalytic [[nucleophile]]. Unlike cysteine and serine, threonine is a [[secondary alcohol]] (i.e. has a methyl group). The methyl group of threonine greatly restricts the possible orientations of triad and substrate, as the methyl clashes with either the enzyme backbone or the histidine base. Consequently, most threonine proteases use an N-terminal threonine in order to avoid such [[steric clash]]es.
Several evolutionarily independent [[enzyme superfamilies]] with different [[protein fold]]s use the N-terminal residue as a nucleophile. This commonality of [[active site]] but difference of protein fold indicates that the active site evolved convergently in those families.<ref name="Buller&Townsend_2013"/><ref>{{cite journal |last1=Ekici |first1=O. D. |author2=Paetzel, M. |author3=Dalbey, R. E. |title=Unconventional serine proteases: variations on the catalytic Ser/His/Asp triad configuration |journal=Protein Science |date=December 2008 |volume=17 |issue=12 |pages=2023–37 |pmid=18824507 |doi=10.1110/ps.035436.108 |pmc=2590910}}</ref>

====Cone snail and fish insulin====

''[[Conus geographus]]'' produces a distinct form of [[insulin]] that is more similar to fish insulin protein sequences than to insulin from more closely related molluscs, suggesting convergent evolution,<ref>{{cite journal |last1=Safavi-Hemami |first1=Helena |last2=Gajewiak |first2=Joanna |last3=Karanth |first3=Santhosh |last4=Robinson |first4=Samuel D. |last5=Ueberheide |first5=Beatrix |last6=Douglass |first6=Adam D. |last7=Schlegel |first7=Amnon |last8=Imperial |first8=Julita S. |last9=Watkins |first9=Maren |last10=Bandyopadhyay |first10=Pradip K. |last11=Yandell |first11=Mark |last12=Li |first12=Qing |last13=Purcell |first13=Anthony W. |last14=Norton |first14=Raymond S. |last15=Ellgaard |first15=Lars |last16=Olivera |first16=Baldomero M. |display-authors=3 |title=Specialized insulin is used for chemical warfare by fish-hunting cone snails |journal=Proceedings of the National Academy of Sciences |date=10 February 2015 |volume=112 |issue=6 |pages=1743–1748 |doi=10.1073/pnas.1423857112|pmid=25605914 |pmc=4330763 |bibcode=2015PNAS..112.1743S |doi-access=free }}</ref> though with the possibility of [[horizontal gene transfer]].<ref>{{cite journal | title=Evidence for a natural gene-transfer from the ponyfish to its bioluminescent bacterial symbiont ''Photobacter leiognathi'' — the close relationship between bacteriocuprein and the copper-zinc superoxide-dismutase of teleost fishes |last1=Martin |first1=J. P. |last2=Fridovich |first2=I. |journal=J. Biol. Chem. |year=1981 |volume=256 |issue=12 |pages=6080–6089 |doi=10.1016/S0021-9258(19)69131-3 |pmid=6787049 |doi-access=free}}</ref>

==== Ferrous iron uptake via protein transporters in land plants and chlorophytes ====

Distant homologues of the metal ion transporters [[Zinc transporter protein|ZIP]] in [[land plants]] and [[chlorophytes]] have converged in structure, likely to take up Fe<sup>2+</sup> efficiently. The IRT1 proteins from ''[[Arabidopsis thaliana]]'' and [[rice]] have extremely different amino acid sequences from ''[[Chlamydomonas]]''{{'}}s IRT1, but their three-dimensional structures are similar, suggesting convergent evolution.<ref>{{Cite journal |last1=Rodrigues |first1=Wenderson Felipe Costa |last2=Lisboa |first2=Ayrton Breno P. |last3=Lima |first3=Joni Esrom |last4=Ricachenevsky |first4=Felipe Klein |last5=Del-Bem |first5=Luiz-Eduardo |date=2023-01-10 |title=Ferrous iron uptake via IRT1 / ZIP evolved at least twice in green plants |journal=New Phytologist |volume=237 |issue=6 |pages=1951–1961 |doi=10.1111/nph.18661 |pmid=36626937 |doi-access=free }}</ref>

====Na<sup>+</sup>,K<sup>+</sup>-ATPase and Insect resistance to cardiotonic steroids ====

Many examples of convergent evolution exist in insects in terms of developing resistance at a molecular level to toxins. One well-characterized example is the evolution of resistance to cardiotonic steroids (CTSs) via amino acid substitutions at well-defined positions of the α-subunit of [[Na+/K+-ATPase|Na<sup>+</sup>,K<sup>+</sup>-ATPase]] (ATPalpha). Variation in ATPalpha has been surveyed in various CTS-adapted species spanning six insect orders.<ref name="Zhen_et_al_2012">{{cite journal |last1=Zhen |first1=Ying |last2=Aardema |first2=Matthew L. |last3=Medina |first3=Edgar M.|last4=Schumer|first4=Molly|last5=Andolfatto |first5=Peter|date=2012-09-28|title=Parallel Molecular Evolution in an Herbivore Community |journal=Science |volume=337 |issue=6102 |pages=1634–1637 |doi=10.1126/science.1226630 |pmid=23019645 |pmc=3770729 |bibcode=2012Sci...337.1634Z}}</ref><ref>Dobler, S., Dalla, S., Wagschal, V., & Agrawal, A. A. (2012). Community-wide convergent evolution in insect adaptation to toxic cardenolides by substitutions in the Na,K-ATPase. Proceedings of the National Academy of Sciences, 109(32), 13040–13045. https://doi.org/10.1073/pnas.1202111109</ref><ref name="Yang_et_al_2019">{{cite journal |last1=Yang |first1=L. |last2=Ravikanthachari|first2=N|last3=Mariño-Pérez|first3=R|last4=Deshmukh|first4=R|last5=Wu |first5=M. |last6=Rosenstein |first6=A. |last7=Kunte|first7=K. |last8=Song |first8=H. |last9=Andolfatto |first9=P. |display-authors=3 |title=Predictability in the evolution of Orthopteran cardenolide insensitivity |journal=Philosophical Transactions of the Royal Society of London, Series B |date=2019 |volume=374 |issue=1777 |pages=20180246 |doi=10.1098/rstb.2018.0246 |pmid=31154978 |pmc=6560278}}</ref> Among 21 CTS-adapted species, 58 (76%) of 76 amino acid substitutions at sites implicated in CTS resistance occur in parallel in at least two lineages.<ref name="Yang_et_al_2019"/> 30 of these substitutions (40%) occur at just two sites in the protein (positions 111 and 122). CTS-adapted species have also recurrently evolved [[Neofunctionalization|neo-functionalized]] duplications of ATPalpha, with convergent tissue-specific expression patterns.<ref name="Zhen_et_al_2012"/><ref name="Yang_et_al_2019"/>

===Nucleic acids===

Convergence occurs at the level of [[DNA]] and the [[amino acid]] sequences produced by [[translation (biology)|translating]] [[structural gene]]s into [[protein]]s. Studies have found convergence in amino acid sequences in echolocating bats and the dolphin;<!--<ref name="Parkeretal2013">{{cite journal | doi=10.1038/nature12511 | last1=Parker | first1=J. | last2=Tsagkogeorga | first2=G | last3=Cotton | first3=J. A. | last4=Liu | first4=Y. | last5=Provero | first5=P. | last6=Stupka | first6=E. | last7= Rossiter | first7=S. J. | year=2013 | title=Genome-wide signatures of convergent evolution in echolocating mammals | journal=Nature | volume=502 | pages=228–231 | issue=7470 |bibcode=2013Natur.502..228P | pmc=3836225 | pmid=24005325}}</ref> may be unreliable per talk page--><ref name="LiuQi2014">{{cite journal |last1=Liu |first1=Zhen |last2=Qi |first2=Fei-Yan |last3=Zhou |first3=Xin |last4=Ren |first4=Hai-Qing |last5=Shi |first5=Peng |title=Parallel Sites Implicate Functional Convergence of the Hearing Gene Prestin among Echolocating Mammals |journal=Molecular Biology and Evolution |volume=31 |issue=9 |year=2014 |pages=2415–2424 |issn=1537-1719 |doi=10.1093/molbev/msu194|pmid=24951728 |doi-access=free }}</ref> among marine mammals;<ref>{{Cite journal |last1=Foote |first1=Andrew D. |last2=Liu |first2=Yue |last3=Thomas |first3=Gregg W. C. |last4=Vinař |first4=Tomáš |last5=Alföldi |first5=Jessica |last6=Deng |first6=Jixin |last7=Dugan |first7=Shannon |last8=Elk |first8=Cornelis E. van |last9=Hunter |first9=Margaret E. |display-authors=3 |date=March 2015 |title=Convergent evolution of the genomes of marine mammals |journal=Nature Genetics |volume=47 |issue=3 |pages=272–275 |doi=10.1038/ng.3198|pmid=25621460 |pmc=4644735 }}</ref> between giant and red pandas;<ref>{{Cite journal |last1=Hu |first1=Yibo |last2=Wu |first2=Qi |last3=Ma |first3=Shuai |last4=Ma |first4=Tianxiao |last5=Shan |first5=Lei |last6=Wang |first6=Xiao |last7=Nie |first7=Yonggang |last8=Ning |first8=Zemin |last9=Yan |first9=Li |date=January 2017 |title=Comparative genomics reveals convergent evolution between the bamboo-eating giant and red pandas |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=114 |issue=5 |pages=1081–1086 |doi=10.1073/pnas.1613870114 |pmc=5293045 |pmid=28096377|bibcode=2017PNAS..114.1081H |doi-access=free }}</ref> and between the thylacine and canids.<ref>{{Cite journal |last1=Feigin |first1=Charles Y. |last2=Newton |first2=Axel H. |last3=Doronina |first3=Liliya |last4=Schmitz |first4=Jürgen |last5=Hipsley |first5=Christy A. |last6=Mitchell |first6=Kieren J. |last7=Gower |first7=Graham |last8=Llamas |first8=Bastien |last9=Soubrier |first9=Julien |display-authors=3 |date=January 2018 |title=Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore |journal=Nature Ecology & Evolution |volume=2 |issue=1 |pages=182–192 |doi=10.1038/s41559-017-0417-y|pmid=29230027 |doi-access=free }}</ref> Convergence has also been detected in a type of [[non-coding DNA]], [[cis-regulatory element]]s, such as in their rates of evolution; this could indicate either [[positive selection]] or relaxed [[Negative selection (natural selection)|purifying selection]].<ref>{{Cite journal |last1=Partha |first1=Raghavendran |last2=Chauhan |first2=Bharesh K |last3=Ferreira |first3=Zelia |last4=Robinson |first4=Joseph D. |last5=Lathrop |first5=Kira |last6=Nischal |first6=Ken K. |last7=Chikina |first7=Maria |last8=Clark |first8=Nathan L. |display-authors=3 |date=October 2017 |title=Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling |journal=eLife |volume=6 |doi=10.7554/eLife.25884|pmid=29035697 |pmc=5643096 |doi-access=free }}</ref><ref>{{cite journal |last1=Sackton |first1=T.B. |last2=Grayson |first2=P. |last3=Cloutier |first3=A. |last4=Hu |first4=Z. |last5=Liu |first5=J.S. |last6=Wheeler |first6=N.E. |last7=Gardner |first7=P.P. |last8=Clarke |first8=J.A. |last9=Baker |first9=A.J. |last10=Clamp |first10=M. |last11=Edwards |first11=S.V. |display-authors=3 |title=Convergent regulatory evolution and loss of flight in paleognathous birds. |journal=Science |date=5 April 2019 |volume=364 |issue=6435 |pages=74–78 |doi=10.1126/science.aat7244 |pmid=30948549 |bibcode=2019Sci...364...74S |s2cid=96435050 |url=http://nrs.harvard.edu/urn-3:HUL.InstRepos:39865637 |doi-access=free }}</ref>